By Matt Smith
Surprise overnight leader Rafael Cabrera-Bello had yet to tee off.
McIlroy may, however, rue a succession of missed long birdie chances as his putting often failed to match his long game.
"I definitely think it could have been better than 65, I missed a putt on the 18th for an eagle, I missed a putt on the first for a birdie that was pretty short," McIlroy, 22, told reporters. "I hit a couple of really good putts on the back nine this morning which could have dropped (in)."
The slight Ulsterman started the day on six under, but this time he played the back nine first and was paired with England's Robert Rock, surprise winner of January's Abu Dhabi championship, and Dubai defending champion Alvaro Quiros.
The trio teed off from the 10th hole early, a wisp of cloud shrouding the desert sun as Dubai slept on Friday, the Muslim holy day.
The back nine of the Majlis course is kinder than the front nine, with three par-fives and a couple of short par-fours, so the players were under pressure to score low early, especially after Carrera-Bello had ended the first round on nine under.
McIlroy sank a birdie on the opening hole after playing a chip shot from the rough to within a few feet of the pin, but at the next hole he came up short with an 18-foot putt that would have earned a second successive birdie.
On the 12th, the trio each had chances to pick up a shot. Quiros was first to try, but the ball curled away from the pin, while McIlroy was inches short with his and Rock also missed.
Rock faded his tee shot into the rough on the next hole, but recovered with a lofted pitch over a cluster of palm trees.
Quiros fared worse. He took a penalty shot after plunging his second shot into the water, then putted for a bogey.
McIlroy then squandered an eagle opportunity, dragging a 25-foot eagle chance to the right of the hole, but he held his nerve for a birdie to move on to eight under.
At the 14th hole, the trio also missed birdie chances as their putting let down some precision approach play. McIlroy consulted caddie J.M. Fitzgerald, whom he credited for his late surge in Thursday's first round, but still his attempt rolled inches wide.
At two under from seven holes, McIlroy seemed frustrated, but on the 17th he sank a 40-foot chip fairway for a birdie.
The U.S. Open champion missed a 10-foot eagle putt on the 18th, but holed for a birdie to be on 10 under at the turn, while on the front nine, he bagged three more to end the round on seven under.
Kaymer scored six under in the opening round and also started Friday from the 10th tee. The German reached nine under with three holes to play before a hole-in-one on the seventh added some gloss to his round.
(Editing by Clare Fallon)